[gmx-users] Normal Mode Analysis in Double-Precision

[Ran Friedman]

Inon Sharony wrote:
> Hi Ran.
> I looked up your suggestions, and got the following:
>
> 0. The parameters in the *.tpr file appear in " 0.00000000e+00 "
> format. How can I tell if this is a float or double? Also, I could not
> see if the position coordinates of the molecule appear in the *.tpr
> file (and if so, if they are in double-precision). Where do the
> coordinates appear? (in the *.gro file only?)
When you run gmxdump it should right e.g.:
Reading file em.tpr, VERSION 3.3.3 (double precision)

As for the coordinates, you have e.g.:
      x[    0]={ 1.35920e+01,  1.80590e+01,  1.79780e+01}
      x[    1]={ 1.31410e+01,  1.77710e+01,  1.75260e+01}
      x[    2]={ 1.30070e+01,  1.78390e+01,  1.68430e+01}

This is double precision. In single precision you'd get only 3 digits,
and the rest will be zeroes.
>
> 1. I do not get any step*.pdb files after the mdrun. In fact, I skip
> the *.pdb file altogether (using PRODRG). Could this be a problem?
It doesn't matter if you use pdb or gro. step*.pdb files are sometimes
given in the output when the system explodes.

It can be that the parameters from PRODRG are not exactly what you want
- you should compare with the force field paramters and charges, though
I'm not sure this can be the source of this behaviour.
>
> 2. The simulation is done in vacuo.
>
> 3. I examined the input *.gro file (as well as the single-precision
> mdruns) using ngmx, and it looks great for those runs that work (i.e.,
> single precision).
>
>
> I will now try repeating the whole minimization-NormalMode process for
> a simple diatomic, to see if I have any problems. Could you send a
> working set of files for me to compare with? Assuming you've run
> Normal Mode analyses in the past...
I'm not sure a diatomic system is good for this - not enough degrees on
freedom.
I'll send you an example made with GMX 3.2.1 - I'm not doing NMA too
often, but it should work.
>
>
> Thanks very much again,
>
> Inon.
>
>
> Quoting "Ran Friedman" <r.friedman at bioc.uzh.ch>:
>
>> Inon Sharony wrote:
>>>
>>>  Hi Ran, thanks for the reply
>>>
>>> I ran "make tests" after compiling with double precision, and it
> came
>>> out fine.
>>>
>>> Could it be that this, second, compilation might have caused some
>>> problems -- I had GROMACS compiled in single-precision, and it
> worked
>>> fine -- could compiling in double-precision after the initial
>>> single-precision overrun some files? I'm not sure anymore...
>>>
>>> Also, the grompp in double-precision works fine (no warnings,
> etc.)
>>> but I get the segfault from mdrun (also in double-precision).
>>> Sometimes this happens in the first minimization step, and
> sometimes
>>> in the second. I was told that this might hint that the input
> file/s
>>> (e.g. the *.gro file) were input in single- and not
> double-precision.
>>> However, since the files have coordinates written in nanometers to
>>> four significant digits, I can't see how the input numbers could
> be in
>>> single or double precision. It was suggested that I insert a
> "print to
>>> screen" line in the source code immediately after the *.gro file
> is
>>> read, to see if the printed data is in single-precision or
>>> double-precision format. What do you think?
>>>
>> The tpr should contain the data in double precision. You can check
> this
>> with gmxdump.
>>
>> Other things that you may want to consider:
>>
>> 1. Do you get step*.pdb files after running mdrun? This may point
> out to
>> something wrong in the input.
>> 2. Are you using a solvated system? Normally NMA is done in vacuo,
> maybe
>> with some scaling of the dielectric.
>> 3. Did you examine the system that you use in the input? Does it
> make
>> sense to you?
>>
>> Ran.
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>
> --Inon   Sharony
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